Sign upLogin

zincware/MDSuite

View on GitHub
Star

Showing 113 of 113 total issues

Similar blocks of code found in 2 locations. Consider refactoring.
Open

def test_translational_dipole_moment():
    trafo = tdp.TranslationalDipoleMoment()
    assert trafo.output_property == mdsuite_properties.translational_dipole_moment

    n_part = 5
Severity: Major
Found in CI/unit_tests/transformations/test_transformations.py and 1 other location - About 1 day to fix
CI/unit_tests/transformations/test_transformations.py on lines 59..79

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 193.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

def test_ionic_current():
    trafo = ionic_current.IonicCurrent()
    assert trafo.output_property == mdsuite_properties.ionic_current

    n_part = 5
Severity: Major
Found in CI/unit_tests/transformations/test_transformations.py and 1 other location - About 1 day to fix
CI/unit_tests/transformations/test_transformations.py on lines 124..144

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 193.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

File radial_distribution_function.py has 713 lines of code (exceeds 250 allowed). Consider refactoring.
Open

"""
MDSuite: A Zincwarecode package.

License
-------
Severity: Major
Found in mdsuite/calculators/radial_distribution_function.py - About 1 day to fix

    Similar blocks of code found in 2 locations. Consider refactoring.
    Open

        def test_correlate(self):
        """
        Test the correlate helper function.

        Returns
    Severity: Major
    Found in CI/unit_tests/utils/test_calculator_helper_methods.py and 1 other location - About 1 day to fix
    CI/unit_tests/utils/test_calculator_helper_methods.py on lines 103..133

    Duplicated Code

    Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

    Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

    When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

    Tuning

    This issue has a mass of 177.

    We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

    The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

    If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

    See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

    Refactorings

    Further Reading

    Similar blocks of code found in 2 locations. Consider refactoring.
    Open

        def test_msd_operation(self):
        """
        Test the msd helper function.

        Returns
    Severity: Major
    Found in CI/unit_tests/utils/test_calculator_helper_methods.py and 1 other location - About 1 day to fix
    CI/unit_tests/utils/test_calculator_helper_methods.py on lines 71..101

    Duplicated Code

    Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

    Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

    When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

    Tuning

    This issue has a mass of 177.

    We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

    The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

    If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

    See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

    Refactorings

    Further Reading

    File simulation_database.py has 572 lines of code (exceeds 250 allowed). Consider refactoring.
    Open

    """
MDSuite: A Zincwarecode package.

License
-------
    Severity: Major
    Found in mdsuite/database/simulation_database.py - About 1 day to fix

      File experiment.py has 554 lines of code (exceeds 250 allowed). Consider refactoring.
      Open

      """
MDSuite: A Zincwarecode package.

License
-------
      Severity: Major
      Found in mdsuite/experiment/experiment.py - About 1 day to fix

        File transformations.py has 537 lines of code (exceeds 250 allowed). Consider refactoring.
        Open

        """
MDSuite: A Zincwarecode package.

License
-------
        Severity: Major
        Found in mdsuite/transformations/transformations.py - About 1 day to fix

          File angular_distribution_function.py has 495 lines of code (exceeds 250 allowed). Consider refactoring.
          Open

          """
MDSuite: A Zincwarecode package.

License
-------
          Severity: Minor
          Found in mdsuite/calculators/angular_distribution_function.py - About 7 hrs to fix

            Function batch_generator has a Cognitive Complexity of 48 (exceeds 5 allowed). Consider refactoring.
            Open

                def batch_generator(  # noqa: C901
        self,
        dictionary: bool = False,
        system: bool = False,
        remainder: bool = False,
            Severity: Minor
            Found in mdsuite/database/data_manager.py - About 7 hrs to fix

            Cognitive Complexity

            Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

            A method's cognitive complexity is based on a few simple rules:

            • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
            • Code is considered more complex for each "break in the linear flow of the code"
            • Code is considered more complex when "flow breaking structures are nested"

            Further reading

            File meta_functions.py has 433 lines of code (exceeds 250 allowed). Consider refactoring.
            Open

            """
MDSuite: A Zincwarecode package.

License
-------
            Severity: Minor
            Found in mdsuite/utils/meta_functions.py - About 6 hrs to fix

              File nernst_einstein_ionic_conductivity.py has 352 lines of code (exceeds 250 allowed). Consider refactoring.
              Open

              """
MDSuite: A Zincwarecode package.

License
-------
              Severity: Minor
              Found in mdsuite/calculators/nernst_einstein_ionic_conductivity.py - About 4 hrs to fix

                File molecular_graph.py has 351 lines of code (exceeds 250 allowed). Consider refactoring.
                Open

                """
MDSuite: A Zincwarecode package.

License
-------
                Severity: Minor
                Found in mdsuite/graph_modules/molecular_graph.py - About 4 hrs to fix

                  File experiment_database.py has 347 lines of code (exceeds 250 allowed). Consider refactoring.
                  Open

                  """
MDSuite: A Zincwarecode package.

License
-------
                  Severity: Minor
                  Found in mdsuite/database/experiment_database.py - About 4 hrs to fix

                    File trajectory_calculator.py has 340 lines of code (exceeds 250 allowed). Consider refactoring.
                    Open

                    """
MDSuite: A Zincwarecode package.

License
-------
                    Severity: Minor
                    Found in mdsuite/calculators/trajectory_calculator.py - About 4 hrs to fix

                      RunComputation has 32 functions (exceeds 20 allowed). Consider refactoring.
                      Open

                      class RunComputation:
    """Collection of all calculators that can be used by an experiment."""

    def __init__(
        self, experiment: Experiment = None, experiments: List[Experiment] = None
                      Severity: Minor
                      Found in mdsuite/experiment/run.py - About 4 hrs to fix

                        File coordination_number_calculation.py has 325 lines of code (exceeds 250 allowed). Consider refactoring.
                        Open

                        """
MDSuite: A Zincwarecode package.

License
-------
                        Severity: Minor
                        Found in mdsuite/calculators/coordination_number_calculation.py - About 3 hrs to fix

                          File memory_manager.py has 319 lines of code (exceeds 250 allowed). Consider refactoring.
                          Open

                          """
MDSuite: A Zincwarecode package.

License
-------
                          Severity: Minor
                          Found in mdsuite/memory_management/memory_manager.py - About 3 hrs to fix

                            File potential_of_mean_force.py has 308 lines of code (exceeds 250 allowed). Consider refactoring.
                            Open

                            """
MDSuite: A Zincwarecode package.

License
-------
                            Severity: Minor
                            Found in mdsuite/calculators/potential_of_mean_force.py - About 3 hrs to fix

                              File data_manager.py has 304 lines of code (exceeds 250 allowed). Consider refactoring.
                              Open

                              """
MDSuite: A Zincwarecode package.

License
-------
                              Severity: Minor
                              Found in mdsuite/database/data_manager.py - About 3 hrs to fix
                                Severity
                                Category
                                Status
                                Source
                                Language